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repository related classes updated

This commit is contained in:
lucio 2024-04-05 21:11:04 +02:00
parent 32b35e4060
commit 38874c9529
29 changed files with 367 additions and 343 deletions
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4
buildImageAndStart.sh
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@ -10,6 +10,6 @@ compile=false
mvn clean package
docker-compose -f docker-compose-standalone build
docker-compose -f docker-compose-standalone.yml build
docker-compose -f docker-compose-standalone up
docker-compose -f docker-compose-standalone.yml up

4
docker-compose-standalone.yml
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@ -14,9 +14,9 @@ services:
ports:
- '5423:5432'
volumes:
- /data/postgres-data:/var/lib/postgresql/data
- ./data/postgres-data:/var/lib/postgresql/data
copy the sql script to create tables
- /data/sql/create_tables.sql:/docker-entrypoint-initdb.d/create_tables.sql
- ./data/sql/create_tables.sql:/docker-entrypoint-initdb.d/create_tables.sql
storagehub:
build:
dockerfile: Dockerfile-standalone

9
gcube/extra-resources/WEB-INF/beans.xml
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@ -10,10 +10,9 @@
SPDX-License-Identifier: BSD-3-Clause
-->
<beans xmlns="https://jakarta.ee/xml/ns/jakartaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
version="4.0" bean-discovery-mode="all">
<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://xmlns.jcp.org/xml/ns/javaee"
xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
http://xmlns.jcp.org/xml/ns/javaee/beans_2_0.xsd"
bean-discovery-mode="all">
</beans>

6
pom.xml
View File

@ -222,11 +222,13 @@
<groupId>org.glassfish.jersey.ext.cdi</groupId>
<artifactId>jersey-cdi1x-servlet</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.jboss.weld.se/weld-se-core -->
<dependency>
<groupId>org.jboss.weld.servlet</groupId>
<artifactId>weld-servlet-core</artifactId>
<groupId>org.jboss.weld.se</groupId>
<artifactId>weld-se-core</artifactId>
<version>5.1.2.Final</version>
</dependency>
<!--
https://mvnrepository.com/artifact/org.glassfish.jersey.core/jersey-common -->
<dependency>

13
src/main/java/org/gcube/data/access/storagehub/MyApplicationListener.java
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@ -1,10 +1,6 @@
package org.gcube.data.access.storagehub;
import jakarta.inject.Inject;
import jakarta.ws.rs.ext.Provider;
import org.apache.jackrabbit.api.JackrabbitRepository;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.glassfish.jersey.server.monitoring.ApplicationEvent;
import org.glassfish.jersey.server.monitoring.ApplicationEventListener;
import org.glassfish.jersey.server.monitoring.RequestEvent;
@ -12,20 +8,21 @@ import org.glassfish.jersey.server.monitoring.RequestEventListener;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import jakarta.ws.rs.ext.Provider;
@Provider
public class MyApplicationListener implements ApplicationEventListener {
private static final Logger log = LoggerFactory.getLogger(MyApplicationListener.class);
@Inject
RepositoryInitializer repository;
StoragehubRepository repository = StoragehubRepository.repository;
@Override
public void onEvent(ApplicationEvent event) {
switch (event.getType()) {
case DESTROY_FINISHED:
log.info("Destroying application storageHub");
((JackrabbitRepository) repository.getRepository()).shutdown();
repository.shutdown();
log.info("Jackrabbit repository stopped");
default:
break;

89
src/main/java/org/gcube/data/access/storagehub/RepositoryInitializerImpl.java
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@ -1,89 +0,0 @@
package org.gcube.data.access.storagehub;
import jakarta.inject.Inject;
import jakarta.inject.Singleton;
import java.nio.file.Path;
import java.nio.file.Paths;
import javax.jcr.Repository;
import javax.jcr.SimpleCredentials;
import javax.naming.Context;
import javax.naming.InitialContext;
import org.apache.jackrabbit.api.JackrabbitRepository;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.gcube.data.access.storagehub.handlers.DataHandler;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.data.access.storagehub.services.admin.InitScript;
import org.gcube.smartgears.ContextProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@Singleton
public class RepositoryInitializerImpl implements RepositoryInitializer{
@Inject
DataHandler dataHandler;
private static Logger log = LoggerFactory.getLogger(RepositoryInitializerImpl.class);
private static RepositoryInitializer instance = new RepositoryInitializerImpl();
public static RepositoryInitializer get(){
return instance;
}
private Repository repository;
private boolean jackrabbitInitialized = false;
@Override
public Repository getRepository(){
return repository;
}
protected RepositoryInitializerImpl(){
try {
InitialContext context = new InitialContext();
Context environment = (Context) context.lookup("java:comp/env");
repository = (Repository) environment.lookup("jcr/repository");
}catch (Throwable e) {
log.error("error initializing repository", e);
throw new RuntimeException("error initializing repository",e);
}
}
public void shutdown() {
((JackrabbitRepository)repository).shutdown();
}
@Override
public synchronized void initContainerAtFirstStart(SimpleCredentials credentials) {
try {
log.info("credential are {} {}",credentials.getUserID(), new String(credentials.getPassword()));
JackrabbitSession ses = (JackrabbitSession) repository.login(credentials);
try {
boolean notAlreadyDone = !jackrabbitInitialized && !ses.getRootNode().hasNode("Home");
if (notAlreadyDone) {
new InitScript().init(ses);
Path shubSpecificConf = ContextProvider.get().appSpecificConfigurationFolder();
Path importPath = Paths.get(shubSpecificConf.toString(), "import" );
Path mainFileImportPath = Paths.get(importPath.toString(), "data.json" );
if (importPath.toFile().exists() && mainFileImportPath.toFile().exists() ) {
//TODO: do import
}
}
else log.info("jackrabbit is already initialized");
}finally {
ses.logout();
}
} catch (Exception e) {
log.warn("error initialising Jackrabbit",e);
}
jackrabbitInitialized = true;
}
}

98
src/main/java/org/gcube/data/access/storagehub/StorageHubApplicationManager.java Normal file
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@ -0,0 +1,98 @@
package org.gcube.data.access.storagehub;
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import javax.jcr.RepositoryException;
import javax.jcr.Session;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
import org.gcube.common.storagehub.model.exporter.DumpData;
import org.gcube.data.access.storagehub.handlers.DataHandler;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.smartgears.ApplicationManager;
import org.gcube.smartgears.ContextProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class StorageHubApplicationManager implements ApplicationManager {
private static Logger logger = LoggerFactory.getLogger(StorageHubApplicationManager.class);
private boolean alreadyShutDown = false;
private boolean alreadyInit = false;
private StoragehubRepository repository;
// private static NotificationClient notificationClient;
/*
* public static NotificationClient getNotificationClient() { return
* notificationClient; }
*/
public StorageHubApplicationManager() {
repository = StoragehubRepository.repository;
}
@Override
public synchronized void onInit() {
logger.info("onInit Called on storagehub");
try {
if (!alreadyInit) {
logger.info("jackrabbit initialization started");
repository.initContainerAtFirstStart();
DataHandler dh = new DataHandler();
Path shubSpecificConf = ContextProvider.get().appSpecificConfigurationFolder();
Path importPath = Paths.get(shubSpecificConf.toString(), "import");
Path mainFileImportPath = Paths.get(importPath.toString(), "data.json");
if (importPath.toFile().exists() && mainFileImportPath.toFile().exists()) {
Session session = null;
try {
ObjectMapper mapper = new ObjectMapper();
DumpData data = mapper.readValue(mainFileImportPath.toFile(), DumpData.class);
session = repository.getRepository().login();
dh.importData((JackrabbitSession) session, data);
session.save();
} catch (RepositoryException e) {
logger.error("error importing data", e);
} catch (IOException je) {
logger.error("error parsing json data, invalid schema file", je);
} finally {
if (session != null)
session.logout();
}
}
alreadyInit = true;
}
} catch (Throwable e) {
logger.error("unexpected error initiliazing storagehub", e);
}
}
@Override
public synchronized void onShutdown() {
if (!alreadyShutDown)
try {
logger.info("jackrabbit is shutting down");
repository.shutdown();
alreadyShutDown = true;
} catch (Exception e) {
logger.warn("the database was not shutdown properly", e);
}
}
}

63
src/main/java/org/gcube/data/access/storagehub/StorageHubAppllicationManager.java
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@ -1,63 +0,0 @@
package org.gcube.data.access.storagehub;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.smartgears.ApplicationManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class StorageHubAppllicationManager implements ApplicationManager {
private static Logger logger = LoggerFactory.getLogger(StorageHubAppllicationManager.class);
private boolean alreadyShutDown = false;
private boolean alreadyInit = false;
private static RepositoryInitializer repository = RepositoryInitializerImpl.get();
//private static NotificationClient notificationClient;
public static RepositoryInitializer getRepository() {
return repository;
}
/*
public static NotificationClient getNotificationClient() {
return notificationClient;
}*/
@Override
public synchronized void onInit() {
logger.info("initializing storagehub");
try {
if (!alreadyInit) {
logger.info("jackrabbit initialization started");
repository.initContainerAtFirstStart(Constants.JCR_CREDENTIALS);
//notificationClient = new NotificationClient();
alreadyInit = true;
}
} catch (Throwable e) {
logger.error("unexpected error initiliazing storagehub",e);
}
}
@Override
public synchronized void onShutdown() {
if (!alreadyShutDown)
try {
logger.info("jackrabbit is shutting down");
repository.shutdown();
alreadyShutDown= true;
} catch (Exception e) {
logger.warn("the database was not shutdown properly",e);
}
}
}

3
src/main/java/org/gcube/data/access/storagehub/handlers/DataHandler.java
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@ -10,7 +10,6 @@ import javax.jcr.RepositoryException;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.gcube.common.storagehub.model.acls.ACL;
import org.gcube.common.storagehub.model.acls.AccessType;
import org.gcube.common.storagehub.model.exceptions.BackendGenericError;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.exporter.DumpData;
import org.gcube.common.storagehub.model.exporter.GroupData;
@ -73,7 +72,7 @@ public class DataHandler {
return data;
}
public void importData(JackrabbitSession session, DumpData data) throws RepositoryException, BackendGenericError {
public void importData(JackrabbitSession session, DumpData data) {
data.getUsers().forEach(u -> {
try {
userHandler.createUser(session, u.getUserName(), "pwd");

5
src/main/java/org/gcube/data/access/storagehub/handlers/vres/VREManager.java
View File

@ -24,7 +24,7 @@ import org.gcube.common.storagehub.model.items.Item;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.handlers.items.Node2ItemConverter;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.delegates.GroupManagerDelegate;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -39,8 +39,7 @@ public class VREManager {
private Map<String, VRE> vreMap = new HashMap<>();
@Inject
RepositoryInitializer repository;
StoragehubRepository repository = StoragehubRepository.repository;
@Inject
Node2ItemConverter node2Item;

9
src/main/java/org/gcube/data/access/storagehub/health/JCRRepositoryCheck.java
View File

@ -6,11 +6,14 @@ import javax.jcr.Session;
import org.gcube.common.health.api.HealthCheck;
import org.gcube.common.health.api.ReadinessChecker;
import org.gcube.common.health.api.response.HealthCheckResponse;
import org.gcube.data.access.storagehub.RepositoryInitializerImpl;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
@ReadinessChecker
public class JCRRepositoryCheck implements HealthCheck{
StoragehubRepository repository = StoragehubRepository.repository;
@Override
public String getName() {
return "Jackrabbit repository";
@ -19,7 +22,7 @@ public class JCRRepositoryCheck implements HealthCheck{
@Override
public HealthCheckResponse check() {
try {
Session session = RepositoryInitializerImpl.get().getRepository().login();
Session session = repository.getRepository().login();
if (session != null) session.logout();
return HealthCheckResponse.builder(getName()).up().build();
}catch (LoginException e) { }

111
src/main/java/org/gcube/data/access/storagehub/repository/JackrabbitRepositoryImpl.java Normal file
View File

@ -0,0 +1,111 @@
package org.gcube.data.access.storagehub.repository;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.Charset;
import javax.jcr.Repository;
import javax.jcr.Session;
import javax.jcr.nodetype.NodeType;
import javax.naming.Context;
import javax.naming.InitialContext;
import org.apache.jackrabbit.api.JackrabbitRepository;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.apache.jackrabbit.api.JackrabbitWorkspace;
import org.apache.jackrabbit.api.security.authorization.PrivilegeManager;
import org.apache.jackrabbit.commons.cnd.CndImporter;
import org.gcube.data.access.storagehub.Constants;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import jakarta.enterprise.context.ApplicationScoped;
@ApplicationScoped
public class JackrabbitRepositoryImpl implements StoragehubRepository {
private static final Logger log = LoggerFactory.getLogger(JackrabbitRepositoryImpl.class);
private Repository repository;
public JackrabbitRepositoryImpl(){
try {
InitialContext context = new InitialContext();
Context environment = (Context) context.lookup("java:comp/env");
repository = (Repository) environment.lookup("jcr/repository");
}catch (Throwable e) {
log.error("error initializing repository", e);
throw new RuntimeException("error initializing repository",e);
}
}
@Override
public Repository getRepository() {
return repository;
}
private boolean jackrabbitInitialized = false;
@Override
public synchronized void initContainerAtFirstStart() {
try {
JackrabbitSession ses = (JackrabbitSession) this.repository.login(Constants.JCR_CREDENTIALS);
try {
boolean notAlreadyDone = !jackrabbitInitialized && !ses.getRootNode().hasNode("Home");
if (notAlreadyDone)
this.init(ses);
else log.info("jackrabbit is already initialized");
}finally {
ses.logout();
}
} catch (Exception e) {
log.warn("error initialising Jackrabbit",e);
}
jackrabbitInitialized = true;
}
@Override
public void shutdown() {
((JackrabbitRepository)repository).shutdown();
}
public void init(JackrabbitSession ses) throws Exception{
log.info("init started");
try {
initNodeTypes(ses);
ses.getRootNode().addNode("Home");
ses.getRootNode().addNode("Share");
PrivilegeManager pm = ((JackrabbitWorkspace) ses.getWorkspace()).getPrivilegeManager();
pm.registerPrivilege("hl:writeAll", false, new String[0]);
ses.save();
}catch (Exception e) {
log.error("init error", e);
throw e;
}
log.info("init finished");
}
void initNodeTypes(Session ses) throws Exception{
InputStream stream = this.getClass().getResourceAsStream("/init/NodeType.cnd");
if (stream == null)
throw new Exception("NodeType.cnd inputStream is null");
InputStreamReader inputstream = new InputStreamReader(stream, Charset.forName("UTF-8"));
// Register the custom node types defined in the CND file, using JCR Commons CndImporter
log.info("start to register the custom node types defined in the CND file...");
NodeType[] nodeTypes = CndImporter.registerNodeTypes(inputstream, ses, true);
for (NodeType nt : nodeTypes)
log.info("Registered: {} ", nt.getName());
log.info("custom node types registered");
}
}

14
src/main/java/org/gcube/data/access/storagehub/repository/StoragehubRepository.java Normal file
View File

@ -0,0 +1,14 @@
package org.gcube.data.access.storagehub.repository;
import javax.jcr.Repository;
public interface StoragehubRepository {
static final StoragehubRepository repository = new JackrabbitRepositoryImpl();
Repository getRepository();
void shutdown();
void initContainerAtFirstStart();
}

9
src/main/java/org/gcube/data/access/storagehub/services/ACLManager.java
View File

@ -23,10 +23,11 @@ import org.gcube.common.storagehub.model.types.ACLList;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.handlers.ACLHandler;
import org.gcube.data.access.storagehub.handlers.UnshareHandler;
import org.gcube.data.access.storagehub.handlers.items.Node2ItemConverter;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.interfaces.ACLManagerInterface;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -53,7 +54,7 @@ import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
@Path("items")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})
@ -61,14 +62,12 @@ public class ACLManager extends Impersonable {
private static final Logger log = LoggerFactory.getLogger(ACLManager.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
StoragehubRepository repository = StoragehubRepository.repository;
@Inject
ACLHandler aclHandler;
@RequestScoped
@PathParam("id")

7
src/main/java/org/gcube/data/access/storagehub/services/GroupManager.java
View File

@ -19,7 +19,8 @@ import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.exceptions.UserNotAuthorizedException;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.delegates.GroupManagerDelegate;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -47,7 +48,7 @@ import jakarta.ws.rs.core.Response;
@Path("groups")
@Singleton
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})
@ -56,7 +57,7 @@ public class GroupManager {
private static final Logger log = LoggerFactory.getLogger(GroupManager.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
GroupManagerDelegate groupHandler;

2
src/main/java/org/gcube/data/access/storagehub/services/Impersonable.java
View File

@ -8,6 +8,7 @@ import org.gcube.common.security.providers.SecretManagerProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import jakarta.enterprise.context.ApplicationScoped;
import jakarta.enterprise.context.RequestScoped;
import jakarta.inject.Inject;
import jakarta.servlet.http.HttpServletRequest;
@ -15,6 +16,7 @@ import jakarta.ws.rs.Path;
import jakarta.ws.rs.core.Context;
@Path("")
@ApplicationScoped
public abstract class Impersonable {
Logger log = LoggerFactory.getLogger(Impersonable.class);

4
src/main/java/org/gcube/data/access/storagehub/services/ItemSharing.java
View File

@ -31,12 +31,12 @@ import org.gcube.common.storagehub.model.types.PrimaryNodeType;
import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.handlers.UnshareHandler;
import org.gcube.data.access.storagehub.handlers.items.Item2NodeConverter;
import org.gcube.data.access.storagehub.handlers.items.Node2ItemConverter;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.smartgears.utils.InnerMethodName;
import org.glassfish.jersey.media.multipart.FormDataParam;
import org.slf4j.Logger;
@ -68,7 +68,7 @@ public class ItemSharing extends Impersonable{
private static final Logger log = LoggerFactory.getLogger(ItemSharing.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
AccountingHandler accountingHandler;

9
src/main/java/org/gcube/data/access/storagehub/services/ItemsCreator.java
View File

@ -16,7 +16,7 @@ import org.gcube.common.storagehub.model.exceptions.BackendGenericError;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.items.GCubeItem;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.handlers.items.ItemHandler;
import org.gcube.data.access.storagehub.handlers.items.builders.ArchiveStructureCreationParameter;
import org.gcube.data.access.storagehub.handlers.items.builders.FileCreationParameters;
@ -24,6 +24,7 @@ import org.gcube.data.access.storagehub.handlers.items.builders.FolderCreationPa
import org.gcube.data.access.storagehub.handlers.items.builders.GCubeItemCreationParameters;
import org.gcube.data.access.storagehub.handlers.items.builders.ItemsParameterBuilder;
import org.gcube.data.access.storagehub.handlers.items.builders.URLCreationParameters;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
@ -47,7 +48,7 @@ import jakarta.ws.rs.core.Response;
@Path("items")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})
@ -58,8 +59,8 @@ public class ItemsCreator extends Impersonable{
@Context
ServletContext context;
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
ItemHandler itemHandler;

9
src/main/java/org/gcube/data/access/storagehub/services/ItemsManager.java
View File

@ -42,7 +42,7 @@ import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.Range;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.handlers.ClassHandler;
@ -53,6 +53,7 @@ import org.gcube.data.access.storagehub.handlers.VersionHandler;
import org.gcube.data.access.storagehub.handlers.items.Item2NodeConverter;
import org.gcube.data.access.storagehub.handlers.items.Node2ItemConverter;
import org.gcube.data.access.storagehub.handlers.plugins.StorageOperationMediator;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.types.PublicLink;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -81,7 +82,7 @@ import jakarta.ws.rs.core.Response.Status;
@Path("items")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})
@ -89,8 +90,8 @@ public class ItemsManager extends Impersonable{
private static final Logger log = LoggerFactory.getLogger(ItemsManager.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
AccountingHandler accountingHandler;

14
src/main/java/org/gcube/data/access/storagehub/services/MessageManager.java
View File

@ -35,7 +35,7 @@ import org.gcube.common.storagehub.model.types.MessageList;
import org.gcube.common.storagehub.model.types.NodeProperty;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
@ -43,6 +43,7 @@ import org.gcube.data.access.storagehub.handlers.items.Item2NodeConverter;
import org.gcube.data.access.storagehub.handlers.items.Item2NodeConverter.Values;
import org.gcube.data.access.storagehub.handlers.items.Node2ItemConverter;
import org.gcube.data.access.storagehub.handlers.plugins.StorageBackendHandler;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.types.MessageSharable;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -54,7 +55,6 @@ import com.webcohesion.enunciate.metadata.rs.RequestHeaders;
import jakarta.enterprise.context.RequestScoped;
import jakarta.inject.Inject;
import jakarta.servlet.ServletContext;
import jakarta.ws.rs.Consumes;
import jakarta.ws.rs.DELETE;
import jakarta.ws.rs.FormParam;
@ -65,13 +65,12 @@ import jakarta.ws.rs.Path;
import jakarta.ws.rs.PathParam;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.QueryParam;
import jakarta.ws.rs.core.Context;
import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
import jakarta.ws.rs.core.Response.Status;
@Path("messages")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})
@ -79,8 +78,8 @@ public class MessageManager extends Impersonable{
private static final Logger log = LoggerFactory.getLogger(MessageManager.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
AccountingHandler accountingHandler;
@ -88,9 +87,6 @@ public class MessageManager extends Impersonable{
@PathParam("id")
String id;
@Context
ServletContext context;
@Inject PathUtil pathUtil;
@Inject Node2ItemConverter node2Item;

13
src/main/java/org/gcube/data/access/storagehub/services/RepositoryInitializer.java
View File

@ -1,13 +0,0 @@
package org.gcube.data.access.storagehub.services;
import javax.jcr.Repository;
import javax.jcr.SimpleCredentials;
public interface RepositoryInitializer {
Repository getRepository();
void initContainerAtFirstStart(SimpleCredentials credentials);
void shutdown();
}

16
src/main/java/org/gcube/data/access/storagehub/services/StorageManager.java
View File

@ -3,14 +3,8 @@ package org.gcube.data.access.storagehub.services;
import java.util.ArrayList;
import java.util.List;
import jakarta.inject.Inject;
import jakarta.ws.rs.GET;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.core.MediaType;
import org.gcube.common.storagehub.model.storages.StorageDescriptor;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.handlers.plugins.StorageBackendHandler;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -18,8 +12,14 @@ import org.gcube.smartgears.utils.InnerMethodName;
import com.webcohesion.enunciate.metadata.rs.RequestHeader;
import com.webcohesion.enunciate.metadata.rs.RequestHeaders;
import jakarta.inject.Inject;
import jakarta.ws.rs.GET;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.core.MediaType;
@Path("storages")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})

7
src/main/java/org/gcube/data/access/storagehub/services/UserManager.java
View File

@ -13,7 +13,8 @@ import org.gcube.common.storagehub.model.exceptions.IdNotFoundException;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.types.SHUBUser;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.delegates.UserManagerDelegate;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -37,7 +38,7 @@ import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
@Path("users")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader(name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"), })
public class UserManager {
@ -46,7 +47,7 @@ public class UserManager {
private static final Logger log = LoggerFactory.getLogger(UserManager.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
UserManagerDelegate userHandler;

7
src/main/java/org/gcube/data/access/storagehub/services/WorkspaceManager.java
View File

@ -31,7 +31,7 @@ import org.gcube.data.access.storagehub.AuthorizationChecker;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.Range;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.StorageHubApplicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.handlers.PublicLinkHandler;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
@ -42,6 +42,7 @@ import org.gcube.data.access.storagehub.handlers.plugins.StorageBackendHandler;
import org.gcube.data.access.storagehub.handlers.vres.VRE;
import org.gcube.data.access.storagehub.handlers.vres.VREManager;
import org.gcube.data.access.storagehub.query.sql2.evaluators.Evaluators;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.storage.backend.impl.GCubeVolatileStorageBackendFactory;
import org.gcube.smartgears.annotations.ManagedBy;
import org.gcube.smartgears.utils.InnerMethodName;
@ -70,14 +71,14 @@ import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
@Path("/")
@ManagedBy(StorageHubAppllicationManager.class)
@ManagedBy(StorageHubApplicationManager.class)
@RequestHeaders({
@RequestHeader(name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"), })
public class WorkspaceManager extends Impersonable {
private static final Logger log = LoggerFactory.getLogger(WorkspaceManager.class);
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
Evaluators evaluator;

34
src/main/java/org/gcube/data/access/storagehub/services/admin/ExportManager.java
View File

@ -1,34 +0,0 @@
package org.gcube.data.access.storagehub.services.admin;
import static org.gcube.data.access.storagehub.Roles.INFRASTRUCTURE_MANAGER_ROLE;
import org.gcube.common.authorization.control.annotations.AuthorizationControl;
import com.webcohesion.enunciate.metadata.rs.RequestHeader;
import com.webcohesion.enunciate.metadata.rs.RequestHeaders;
import jakarta.ws.rs.Consumes;
import jakarta.ws.rs.POST;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.core.MediaType;
@Path("admin")
@RequestHeaders({
@RequestHeader( name = "Authorization", description = "Bearer token, see https://dev.d4science.org/how-to-access-resources"),
})
public class ExportManager {
@POST
@Path("export")
@AuthorizationControl(allowedRoles = {INFRASTRUCTURE_MANAGER_ROLE})
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.TEXT_PLAIN)
public String export() {
return "";
}
}

60
src/main/java/org/gcube/data/access/storagehub/services/admin/InitScript.java
View File

@ -1,60 +0,0 @@
package org.gcube.data.access.storagehub.services.admin;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.Charset;
import javax.jcr.Session;
import javax.jcr.nodetype.NodeType;
import org.apache.jackrabbit.api.JackrabbitSession;
import org.apache.jackrabbit.api.JackrabbitWorkspace;
import org.apache.jackrabbit.api.security.authorization.PrivilegeManager;
import org.apache.jackrabbit.commons.cnd.CndImporter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class InitScript {
private static Logger log = LoggerFactory.getLogger(InitScript.class);
public void init(JackrabbitSession ses) throws Exception{
log.info("init started");
try {
initNodeTypes(ses);
ses.getRootNode().addNode("Home");
ses.getRootNode().addNode("Share");
PrivilegeManager pm = ((JackrabbitWorkspace) ses.getWorkspace()).getPrivilegeManager();
pm.registerPrivilege("hl:writeAll", false, new String[0]);
ses.save();
}catch (Exception e) {
log.error("init error", e);
throw e;
}
log.info("init finished");
}
void initNodeTypes(Session ses) throws Exception{
InputStream stream = InitScript.class.getResourceAsStream("/init/NodeType.cnd");
if (stream == null)
throw new Exception("NodeType.cnd inputStream is null");
InputStreamReader inputstream = new InputStreamReader(stream, Charset.forName("UTF-8"));
// Register the custom node types defined in the CND file, using JCR Commons CndImporter
log.info("start to register the custom node types defined in the CND file...");
NodeType[] nodeTypes = CndImporter.registerNodeTypes(inputstream, ses, true);
for (NodeType nt : nodeTypes)
log.info("Registered: {} ", nt.getName());
log.info("custom node types registered");
}
}

64
src/main/java/org/gcube/data/access/storagehub/services/admin/ScriptManager.java
View File

@ -18,16 +18,17 @@ import org.gcube.common.authorization.control.annotations.AuthorizationControl;
import org.gcube.common.security.AuthorizedTasks;
import org.gcube.common.security.providers.SecretManagerProvider;
import org.gcube.common.storagehub.model.Paths;
import org.gcube.common.storagehub.model.exporter.DumpData;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.accounting.AccountingHandler;
import org.gcube.data.access.storagehub.handlers.DataHandler;
import org.gcube.data.access.storagehub.handlers.items.ItemHandler;
import org.gcube.data.access.storagehub.handlers.items.builders.FileCreationParameters;
import org.gcube.data.access.storagehub.handlers.items.builders.ItemsParameterBuilder;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.scripting.AbstractScript;
import org.gcube.data.access.storagehub.scripting.ScriptUtil;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.data.access.storagehub.services.admin.ScriptStatus.Status;
import org.gcube.smartgears.ContextProvider;
import org.gcube.smartgears.context.application.ApplicationContext;
@ -37,11 +38,11 @@ import org.glassfish.jersey.media.multipart.FormDataParam;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.webcohesion.enunciate.metadata.rs.RequestHeader;
import com.webcohesion.enunciate.metadata.rs.RequestHeaders;
import jakarta.inject.Inject;
import jakarta.servlet.ServletContext;
import jakarta.ws.rs.Consumes;
import jakarta.ws.rs.DefaultValue;
import jakarta.ws.rs.GET;
@ -50,7 +51,6 @@ import jakarta.ws.rs.Path;
import jakarta.ws.rs.PathParam;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.WebApplicationException;
import jakarta.ws.rs.core.Context;
import jakarta.ws.rs.core.MediaType;
@Path("admin/script")
@ -62,14 +62,11 @@ public class ScriptManager {
private static Logger log = LoggerFactory.getLogger(ScriptManager.class);
private RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
@Inject
AccountingHandler accountingHandler;
@Context
ServletContext context;
@Inject
ScriptUtil scriptUtil;
@ -79,7 +76,7 @@ public class ScriptManager {
@Inject
PathUtil pathUtil;
private static HashMap<String, ScriptStatus> scriptStatusMap = new HashMap<String, ScriptStatus>();
protected static HashMap<String, ScriptStatus> scriptStatusMap = new HashMap<String, ScriptStatus>();
@POST
@Path("execute")
@ -119,6 +116,55 @@ public class ScriptManager {
return status;
}
@POST
@Path("export")
@AuthorizationControl(allowedRoles = {INFRASTRUCTURE_MANAGER_ROLE})
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
public ScriptStatus export() {
InnerMethodName.set("export");
try {
String runningId = UUID.randomUUID().toString();
ApplicationContext appContext = ContextProvider.get();
String serverHost = appContext.container().configuration().hostname();
final ScriptStatus status = new ScriptStatus(runningId, null, serverHost);
scriptStatusMap.put(runningId, status);
Runnable execution = () -> {
JackrabbitSession session = null;
try {
session = (JackrabbitSession) repository.getRepository().login();
DumpData dd = new DataHandler().exportData(session);
ObjectMapper om = new ObjectMapper();
status.setSuccess(om.writeValueAsString(dd));
log.info("""
export finished with result
---------------------------
{}
---------------------------
""", status.getResult());
} catch (Throwable t) {
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw, true);
t.printStackTrace(pw);
status.setFailed(sw.toString());
log.warn("export failed", t);
} finally {
if (session!=null)
session.logout();
}
};
new Thread(execution).start();
return status;
}catch(Exception e) {
throw new WebApplicationException("error starting export", e);
}
}
private Class<?> uploadClass(InputStream stream, ScriptClassLoader classLoader, String name) throws Throwable {
try(ByteArrayOutputStream buffer = new ByteArrayOutputStream()){

22
src/main/java/org/gcube/data/access/storagehub/services/admin/ScriptStatus.java
View File

@ -16,7 +16,7 @@ public class ScriptStatus {
private String errorMessage;
private String resultPath;
private String result;
private long start;
@ -31,7 +31,15 @@ public class ScriptStatus {
this.status = Status.Running;
this.start = System.currentTimeMillis();
this.runningId = runningId;
this.resultPath = resultPath;
this.result = resultPath;
this.executionServer = executionServer;
}
public ScriptStatus(String runningId, String executionServer) {
super();
this.status = Status.Running;
this.start = System.currentTimeMillis();
this.runningId = runningId;
this.executionServer = executionServer;
}
@ -46,6 +54,12 @@ public class ScriptStatus {
this.finished = System.currentTimeMillis();
}
public void setSuccess(String result) {
this.status = Status.Success;
this.finished = System.currentTimeMillis();
this.result = result;
}
public Status getStatus() {
return status;
}
@ -79,8 +93,8 @@ public class ScriptStatus {
return String.format("%d minutes %d seconds", minutes, seconds);
}
public String getResultPath() {
return resultPath;
public String getResult() {
return result;
}
public String getRunningId() {

5
src/main/java/org/gcube/data/access/storagehub/services/delegates/GroupManagerDelegate.java
View File

@ -37,12 +37,11 @@ import org.gcube.common.storagehub.model.types.NodeProperty;
import org.gcube.common.storagehub.model.types.PrimaryNodeType;
import org.gcube.data.access.storagehub.Constants;
import org.gcube.data.access.storagehub.PathUtil;
import org.gcube.data.access.storagehub.StorageHubAppllicationManager;
import org.gcube.data.access.storagehub.Utils;
import org.gcube.data.access.storagehub.handlers.TrashHandler;
import org.gcube.data.access.storagehub.handlers.items.builders.FolderCreationParameters;
import org.gcube.data.access.storagehub.repository.StoragehubRepository;
import org.gcube.data.access.storagehub.services.GroupManager;
import org.gcube.data.access.storagehub.services.RepositoryInitializer;
import org.gcube.data.access.storagehub.services.interfaces.ACLManagerInterface;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -64,7 +63,7 @@ public class GroupManagerDelegate {
@Inject
ACLManagerInterface aclManagerDelegate;
RepositoryInitializer repository = StorageHubAppllicationManager.getRepository();
private final StoragehubRepository repository = StoragehubRepository.repository;
public List<String> getGroups(JackrabbitSession session) throws RepositoryException {
List<String> groups = new ArrayList<>();